[phenixbb] Using Phenix to calculate Atom Maps

Pavel Afonine pafonine at lbl.gov
Sun May 13 23:46:17 PDT 2007

Hi James,

there are some ways of doing this:

1) One can calculate it from the atomic model using the standard 
formulas rho(r)=... . This option is currently not available.

2) One can get (Fcalc, phi_calc) to certain resolution and completeness 
first and then do the Fourier transformation. In this case you will get 
a Fourier image of the "true" electron density (for example, calculated 
in "1)") at given resolution and completeness. Obviously, as higher 
resolution and completeness, as closer this Fourier image to the "true" 
This is possible to do with phenix.refine and the following command will 
do this:

% phenix.refine model.pdb data.mtz main.number_of_macro_cycles=0 
electron_density_map.k=0 electron_density_map.n=-1 

In the example above you basically load the model and data into 
phenix.refine and ask it to do nothing (main.number_of_macro_cycles=0) 
but calculate the k*Fobs-n*Fmodel map with the coefficients k=0 and 
n=-1. Here Fmodel is just Fcalc from atomic model and does not include 
any bulk solvent contribution or other scales (we turned it off with 

Please note that the Fourier image calculated in this example will be 
based on the resolution and completeness of provided Fobs (data.mtz) 
(will be not exactly what one can get with formulas rho(r)=...).

I realize that "2)" is not the best way of doing this but is rather a 
work-around. In future I plan to provide a specific option to do what 
you are asking for: calculate the electron density from atomic model; 
this is in my to-do list. I will also add the example above to 
phenix.refine Manual for the future references.

Please let me know if you have any questions or problems.


James Fraser wrote:
> Hello,
> Is there a way to use Phenix to calculate maps that are just
> representative of the model?
> This would be similar to the ATMMAP mode of SFALL or using
> model_fcalc.inp/model_phase.inp in CNS.
> Thanks,
> James
> _______________________________________________
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> phenixbb at phenix-online.org
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